Figure 4

Clusters of TF binding sites immediately upstream of the transcription start site in 3 genes of cluster set 15 (co-expressed genes with high expression in thymus): The upper panels compare the location of TF binding sites surrounding and upstream regions of transcription start site (based on the corresponding mRNA annotations from NCBI's RefSeq database) of human and mouse Arid1a, Abcg1 and Zfp162 genes in GenomeTrafac database http://genometrafac.cchmc.org. The bottom panels list the gene descriptions and each of the binding sites in their order of occurrence from distal (top) to proximal (bottom) to exon 1 of the human gene, which is on the left within each panel. Binding sites in bold are known "lymphoid elements". The first nucleotide of exon 1 is at bp 40,001. Each of the colored bars represents a class of TF binding sites and connects homologous binding sites in genes of the two species. The orthologous genes may differ in the number and location of specific TF's binding sites. The corresponding coordinates of the regions on human (NCBI Build 35, May 2004) genome assembly are: chr1: 26,706,590–26,706,986 (+), chr21: 42,512,113 42,512,317 (+) and chr11: 64,302,720–64,302,924 (-) for human ARID1A, ABCG1 and SF1 respectively. Coordinates in the mouse genome assemblies (Build 33 Mouse Assembly, May 2004) are: chr4: 132,206,952–132,207,348 (-), chr19: 6,151,958–6,152,162 (+) and chr17: 29,663,342–29,663,546 (+) for Arid1a, Abcg1 and Zfp162 respectively.